The Headteachers' Association of Scotland has warned that, rather than attracting the most disaffected pupils, the skills academies could be a magnet for middle-ability pupils who see the vocational modules as an easier option than more academic subjects which demand more effort.
The association also fears the initiative, part of Labour's manifesto for next May's Scottish general election, could herald a return to old divisions between junior and senior secondary schools.
And the Association of Scotland's Colleges warns that the Labour Party may be looking at Neets (not in education, employment or training) in too narrow a way, seeing prevention as the "only show in town".
Tom Kelly, its chief executive, is concerned that 16 to 21-year-olds may be forgotten in a new focus on the 14 to 16-year-old group to remove them from the risk of not going into education, employment or training when they leave school.
CBI Scotland has offered a broad welcome, as has the Educational Institute of Scotland, which supports attempts to make school-college links work better and is in favour of the skills for work courses.
Speaking at the Labour Party conference last weekend, the First Minister outlined his plans to create between 50 and 100 skills academies in secondary schools and colleges across all local authorities to give Scottish pupils vocational options from the age of 14 - if his party is returned to power at Holyrood.
The main aim is to provide better motivation, relevance and engagement for the potential Neet group. However, they will also be open to students following traditional "academic" courses who want to improve their employability.
Labour sources have told The TESS that the new skills academies are expected to expand significantly the skills for work courses which have already been piloted in schools and colleges; 5,000 pupils at the S3S4 stages are taking the courses this year.
The proposal will mean more choice options for pupils from the age of 14.
Careers advisers - whose role in schools is being expanded - will be expected to step up their guidance. However, if pupils want to retain the "privilege" of remaining on the courses, they will have to meet standards of behaviour and apply themselves to their work.
All pupils will still have to study core literacy, arithmetic and ICT units and they will all have the opportunity to be tested in numeracy and literacy before they leave school.
The choice of the title - skills academies - is intended to signal Labour's intention of raising the status and prestige of vocational education.
Mr McConnell linked his plans to the creation of a full employment agency, which will bring existing agencies together; a refocused Careers Scotland to support young people in school; and a renewed emphasis on functional literacy.
The First Minister also made clear there were two parts to his new mantra.
The skills academies would ensure that "we will leave no child behind," he said, while "we want to hold no young person back either and we will not neglect the youngster who has the potential to be a high achiever".
But Bill McGregor, general secretary of HAS, wondered what the impact will be in a town which has two secondary schools, where only one is turned into a skills academy. "What will parents try to do in a situation like that?"
"In a city, will a skills academy secondary become so focused on skills that it becomes difficult for it to achieve high attainment?"